You're in a rather awkward situation there, Redhorizon! Visitors from the Americas seem to prefer booking their whole 'tour' through one agent, so you either have to have a great deal of trust in that agent, or find another way whereby you can satisfy yourself that all will be well. In the UK there are quite a number of reputable companies which specialise in Egypt, and being British, most of the DE's on this forum can vouch for and recommend them. However, when it comes to the States we don't know them, and are therefore unable to give a personal recommendation.
I think the best advice you'll get from the majority on here, that's if you're not too sure of your US agent, would be to pre-book your flights and a hotel here in Egypt for a few days, and then contact one of the well known Egyptian companies, after all, whichever foreign agent you used would hand your booking over to one of these Egyptian agents anyway; so what have you got to lose?
At least that way you would be able to view the boats before you actually parted with your cash. All the cruise itineraries are almost identical.
Loads of boats aren't sailing due to the low tourist numbers, and passengers are being transferred to alternatives to the one that they originally thought they would be on, so it would be difficult to guarantee exactly which boat you would get otherwise.
Try emailing one or two Egyptian companies, and see what response you get.